Installation on Mac OS X

Git

brew install git
brew install git-flow

https://help.github.com/articles/ignoring-files/#create-a-global-gitignore

git config --global core.excludesfile ~/.gitignore_global
echo ".DS_Store" >> ~/.gitignore_global

Git flow completion

First, install

brew install bash-completion

Then, add to ~/.bash_profile

if [ -f $(brew --prefix)/etc/bash_completion ]; then
  . $(brew --prefix)/etc/bash_completion
fi

Thereafter, restart terminal.

R/Bioconductor

R packages: tidyverse, ProjectTemplate, survival, knitr etc.

https://bioconductor.org/install/

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(c("org.Hs.eg.db", "limma", "edgeR"))

SSH

ssh-keygen
ssh-add ~/.ssh/id_rsa

https://help.github.com/articles/adding-a-new-ssh-key-to-your-github-account/

pbcopy < ~/.ssh/id_rsa.pub

When cloning from a host (github, gitlab, bitbucket, etc.) for the fist time, clone a git repo in the command line; and add to list of known hosts. Thereafter everything works smoothly in RStudio.

Pandoc, LaTex, etc.

brew install pandoc
brew install pandoc-citeproc

lovrot-macbook:~ lovrot$ brew install latex
Error: No available formula with the name "latex"
Installing TeX from source is weird and gross, requires a lot of patches, and only builds 32-bit (and thus can't use Homebrew dependencies)

We recommend using a MacTeX distribution: https://www.tug.org/mactex/

You can install it with Homebrew-Cask:
brew cask install mactex

brew cask install mactex

N.B. Massive.

Miscellaneous

brew cask install java

brew cask install google-chrome
brew cask install owncloud
brew cask install mendeley-reference-manager

brew tap homebrew/science
brew install samtools
brew install picard-tools
brew install igv

Update all packages installed via homebrew

brew update && brew upgrade
brew cask upgrade

lovrot/installation-macosx.md